The archaeal concept and the world it lives in: a retrospective

The archaeal concept and the world it lives in: a retrospective

Carl R. Woese (center) with His Majesty Carl XVI Gustaf of Sweden and Queen Silvia on the occassion of his receiving the 2003 Crafoord
Prize, given by the Royal Swedish Academy of Sciences. Photo credit: Royal Swedish Academy of Sciences.
Photosynthesis Research 80: 361–372, 2004.
© 2004 Kluwer Academic Publishers. Printed in the Netherlands.
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Personal perspective
The archaeal concept and the world it lives in: a retrospective
Carl R. Woese
Department of Microbiology, University of Illinois at Urbana-Champaign, B103 Chemical and Life Sciences
Laboratory, 601 South Goodwin Ave, Urbana, IL 61801-3709, USA (e-mail: carl@phylo.life.uiuc.edu; fax:
+1-217-244-6697)
Received 9 July 2003; accepted in revised form 30 August 2003
Key words: archaea, evolution, genomics, molecular phylogeny, phylogenetic reconstruction, ribosomal RNA
Abstract
The present retrospective concerns the discovery and development of the archaea, the so-called ‘third form of life’
that no one anticipated and many did not, and still do not want. In its birth pangs, which the archaea had a plenty, the
concept encountered biology unmasked; for it ran up against some of the key struts in the 20th century biological
edifice. Consequently, the history of the development of the archaeal concept provides an excellent window on
certain of the weaknesses in the 20th century biology paradigm, weaknesses that have now led that paradigm to a
conceptual dead end. On the other hand, the archaeal concept has also provided us one of the pillars on which a
new holistic paradigm for biology can be built. So, it would seem of value to retrace some of the twists and turns
in the history of the development of the archaeal concept. Given my position vis-à-vis the archaea, my account will
be a personal one.
Introduction
These are strange, unsettled times in biology. Biology
today feels to me like a gigantic engine spinning its
wheels, waiting to do something, anything. The 20th
century in biology has been a time of spectacular advances, almost certainly the most productive period in
biology’s history. Yet it was also a time when the ways
in which biologists thought about biology changed
dramatically. It was a time when the world view of
19th century classical physics imposed itself on biology: reductionism and mechanism are part and parcel
of both genetics and molecular biology, the dominating paradigms of the last century. Under their aegis
biology was reformulated in a remarkably procrustean
fashion. While one cannot deny the tremendous advances that molecular biology (and genetics) wrought,
one can and should decry the price biology paid for
them. A holistic perspective was effectively banished
from biology. The cell was reduced merely to the sum
of its parts – the cell as a whole became no more than
a shadowy backdrop for the molecular drama. The
fact that the cell has an evolutionary dimension, an
understanding of which is essential to genuinely understand the cell, was ignored; the whole of evolution
was dismissed as a collection of meaningless historical
accidents. The study of development, a principal way
in which biologists approached the important problem
of biological form, was squeezed by 20th century genetics into a reductionist gene-centered mode (Gilbert
et al. 1996).
When it was all over, almost every trace of a holistic view of living systems was gone. Yet hardly
anyone paid attention – so riveting and reassuring was
the mechano-reductionist view of biology. One of the
few cries of alarm came from outside biology per se,
from the physicist/philosopher David Bohm, in the
1960s:
It does seem odd . . . that just when physics is
. . . moving away from mechanism, biology and
psychology are moving closer to it. If the trend
continues . . . scientists will be regarding living
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and intelligent beings as mechanical, while they
suppose that inanimate matter is too complex and
subtle to fit into the limited categories of mechanism (Bohm 1969).
So here biology sits, at the beginning of the 21st
century with the major guiding paradigms that shaped
and drove it in the last century out of steam, reduced to
bodies of powerful technique, their vision of the future
gone. What will now define the course of biology?
Will biology become merely the servant of the society,
devoted to solving practical problems? Or will a new
and vibrant holistic paradigm emerge to energize the
field and lead it into an even brighter future?
But first, we need to understand how biology arrived at this conundrum. In this sense, the discovery
of the archaea as a ‘third domain of life’ and the development of the ‘archaeal concept’ are illuminating.
I will use them as a window into the problems emanating from the 20th century biology paradigm, and as
a springboard towards redefining biology for the 21st
century. Of necessity, this account will be a personal
one.
The story for me begins in the 1960s, when my
passing interest in evolution began to intensify and
congeal. At the time the genetic code was all the
rage, following upon the heels of, and being invested with the panache of, James Watson and Francis
Crick’s solving the ‘problem of the gene.’ As originally conceived by George Gamow (1954) the genetic
code was the cryptographic aspect of a fundamental
biology problem. The codons were seen as physically templating their corresponding amino acids. Thus,
to know the codon assignments was to understand
the physical/chemical interactions upon which translation and its evolution were based. However, Crick
and his adaptor hypothesis soon put an end to that
grandiose hope (Crick 1958). Whereas Gamow saw
the codon assignments as absolute, founded in interactions between nucleic acids and amino acids, the
adaptor hypothesis took an opposite tack, viewing the
codon assignments as arbitrary: which amino acid became associated with which adaptor (tRNA) was seen
as merely a matter of historical accident: were the code
to evolve all over again, the codon assignments would
surely be unrelated to those that we know. Since the
adaptor hypothesis gained rapid and essentially universal acceptance, the eventual determination of the
codon assignments ended the matter, solved the problem. The biological significance of the genetic code
lay solely in the catalog of codon assignments per se.
However, I did not see it that way. From the start
I had been skeptical of the adaptor hypothesis. The
idea never really explained or predicted anything; we
were just as ignorant with as without it. What the
adaptor hypothesis did do, however, was spread a veneer of complacency over our ignorance – which, of
course, silenced all further questioning concerning the
nature of ‘sRNA’ (as the tRNA molecule was originally called) (Woese 2001). While Gamow might not
have been right in his speculations about the exact
nature of the code, to me he was on the right track, at
least a track that might lead somewhere. In any case,
a molecule as complex and inherently interesting as
tRNA could not be simply an adaptor for amino acids.
tRNA was far more likely a central functioning part of
the translation mechanism than a passive carrier of the
amino acid into that mechanism (Woese 2001).
It did not feel right that the code was merely an
historical accident. There was too much order in the
set of codon assignments for that; order which had to
be explained. The problem of the genetic code should
never have been formulated in a vacuum in the first
place. The code was manifest materially in the tRNAs,
and to understand how the code evolved, one could
not simply ignore the evolution of the tRNAs, or the
rest of the translation apparatus for that matter. Right
or wrong, this is the argument that convinced me that
the central problem in the evolution of the cell was the
evolution of translation, and from then on this has been
my major, driving concern in biology.
The evolution of translation is what you can call
a non-Darwinian or pre-Darwinian problem; it transcends the biological world known to Charles Darwin
and his contemporaries. The problem I faced was how
to approach the deep evolutionary questions that have
to do with the evolution of the cell itself. At the time
I did not know, and in a sense still do not. But one
thing seemed certain: approaching any questions of
this nature would require a comprehensive phylogeny,
a universal phylogenetic tree, as a conceptual framework. Since no universal phylogeny existed at the time
(our understanding of evolutionary relationships was
effectively confined to plants and animals), realizing
that phylogeny would ‘merely’ require determining
the phylogenetic relationships among the bacteria and
the single celled eukaryotes, and then tying all this into
the phylogenies of animals and plants.
A methodology for doing this, however, was not
in place at the time; but the makings of it were, with
the ‘oligonucleotide cataloging’ approach to RNA sequencing recently developed by Frederick Sanger and
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his colleagues (Sanger et al. 1965). A molecule ideally
suited to both the methodology and the problem, an
excellent potential indicator of phylogenetic relationship (on a global scale), seemed to be ribosomal RNA
(the small subunit rRNA). Ribosomal RNA is ubiquitous, relatively easy to handle, large enough to give
a reliable amount of data, and has evolved relatively
slowly – hopefully slowly enough so that reasonably
good organismal genealogical traces remained across
the entire phylogenetic spectrum (Woese 1987). Also,
rRNA is an integral part of a large molecular complex that is central to the functioning of the cell. In
other words, in that weird world where bacterial genes
seem to be passed around among various species, the
central components of the translation apparatus would
probably be the last genes you would expect to find
transferred laterally (Fox et al. 1977a, b); and as we
now know, this is the case. Ribosomal RNA sequence
comparisons give us the entire genealogical spectrum,
from the ‘root’ of the universal tree on down to the
finer branchings.
It turned out that reworking Sanger’s oligonucleotide cataloging technology to fit our needs was the
least of the problems we would face. At the time I was
totally unaware of the hornet’s nest we were stepping
into with bacterial taxonomy – something that had a
long and sorry history.
To continue the story: the oligonucleotide cataloging methodology was soon ready to go, and we
began (at first very slowly) to turn out rRNA ‘catalogs’
(sets of characteristic oligonucleotides) for a variety
of microorganisms (and a few eukaryotes). In the process, one quickly gained a feel for whether a particular
oligonucleotide catalog represented a ‘prokaryote’ or a
eukaryote (Fox et al. 1980): each grouping had a very
distinctive ‘oligonucleotide signature’ (Woese et al.
1985). Thus you can readily imagine my amazement
when somewhere along the line we ran into a particular catalog (representing Methanobacterium thermoautotrophicum) that had neither the ‘prokaryote’
nor the eukaryote signature. Everyone knew that extant organisms had to be either prokaryotic or eukaryotic, did they not; so how could this be? Our first
thought was experimental error; the wrong RNA molecule had somehow been picked. Repetition of the
experiment ruled this out. And producing catalogs for
relatives of other methanogens quickly showed that
all methanogens behaved similarly; all had this weird
new type of rRNA. Soon the group of methanogens
had an oligonucleotide signature of its own, distinct
from both the ‘prokaryotic’ and the eukaryotic sig-
natures (Fox et al. 1977). The problem was that the
methanogens were classically recognized as ‘prokaryotes.’ How to reconcile all this. Could there possibly
exist organisms that were neither ‘prokaryotes’ nor eukaryotes? The dogma said ‘no,’ but the experiments
suggested ‘yes.’ This was my first (except for the adaptor hypothesis), but definitely not last, encounter
with a major biological dogma, one that had shaped
how all biologists thought about life on earth, and one
that, in being wrong, had caused enormous damage.
But it was not yet the time to attack the dogma publicly. First we had to see whether this strange type of
rRNA occurred elsewhere, in non-methanogenic taxa.
And we soon had the answer: yes, such organisms did
exist. Oligonucleotide cataloging revealed that the socalled extreme halophiles were of this type, as were
two strange ‘thermoacidophiles,’ Thermoplasma and
Sulfolobus (Woese et al. 1978, 1984). At that point it
became apparent that we were dealing with a major
organismal grouping, a collection of highly disparate
phenotypes all of which appeared to have the same
pedigree (Woese 1982).
Still, caution was called for. Before going off on
cloud nine about finding a whole new kingdom of organisms, make sure the organisms in the group have
more in common than just a characteristic ribosomal
RNA. You really cannot make a strong case on the
basis of one trait alone. My main partner in crime at
the time, the microbiologist Ralph Wolfe (in whose
laboratory the methanogens had been grown and radioactively labeled), kept telling me that a stool with
one leg would not stand; you need at least three legs!
(See Figure 1 for the photograph of Wolfe with the
author and Otto Kandler.) What other characteristics
Figure 1. Left to right: the author (Carl Woese), Ralph Wolfe and
Otto Kandler. This photo was taken at Rofan Mountain, Austria,
1981.
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did the members of this group share? It had been
known that the extreme halophiles, the thermoplasmas, and Sulfolobus all had the same kind of very
unusual lipids: the links to glycerol were ether, not
ester; the lipid chains were branched (built of isoprenoid subunits) not straight; and the chirality around
the central carbon of the glycerol moiety was the opposite of what one would expect of a typical lipid
(Woese 1987). [This coincidence had previously been
written off as convergent evolution, the result of all
these organisms individually adapting to an ‘extreme’
environment (Brock 1978).] What was not known at
the time was what sort of lipids the methanogens had.
Ralph Wolfe prepared a goodly amount of a methanogen and the cell mass was shipped to T. Langworthy
for lipid analysis. The answer: methanogens too
have these unusual ether-linked, branched chain lipids (Tornabene and Langworthy 1979). The proverbial
stool now had two legs, and confidence grew. More
legs were soon to come. Members of the archaebacteria (as the archaea were initially called) showed a
variety of cell wall types, but none of them were of
the characteristic bacterial (peptidoglycan-containing)
type (Kandler and Hippe 1977). The DNA-dependent
RNA polymerases of the archaebacteria were atypical, far more like those of the eukaryotes than like
(eu)bacterial RNA polymerases (Huet et al. 1983).
Archaebacteria showed different antibiotic sensitivities than did normal bacteria. And the list of unique
or non-eubacterial characteristics continued to grow
(Woese 1987). For many of us there could no longer
be any doubt that the archaebacteria were a grouping
of organisms unto themselves, neither eubacterial nor
eukaryotic.
That, however, is not how the majority of biologists, especially microbiologists, saw it. I was quite
taken aback by the negative response the initial announcement of the existence of this ‘third form of life’
evoked, and the vehemence of that response! My colleague Ralph Wolfe was telephoned by Nobel laureate
S.E. Luria, who scolded him: ‘Ralph, you must dissociate yourself from this nonsense, or you’re going to
ruin your career!’ (Wolfe 2003). Two of the three main
weekly news magazines in the United States carried
a story about the discovery of the archaebacteria; the
third did not – because, it turns out, the science writer
for that magazine had checked with a microbiologist,
a confidante of his, who had advised him that a ‘third
form of life’ was absurd. There was a notable amount
of behind-the-scenes grumbling by microbiologists as
well; but, strangely, only one biologist had the courage
to challenge the archaeal concept in print at that time
(Steitz 1978).
The bizarre thing about this episode in the history
of the archaea is that the grouping achieved notoriety
not because they represented a third type of living system per se (only the lay scientific public were naive
enough to see it that way), but because their presumed
existence violated a central dogma, the eukaryote–
prokaryote dichotomy. So rather than question the
dogma, most (micro)biologists were content to condemn the finding. Their failure to question that dogma
is one of the black marks in microbiology’s history,
for the prokaryote–eukaryote is a conjecture, a theory – and scientists are supposed to test theories. The
history behind why microbiology did not do this is
an interesting and instructive one, one well worth our
considering.
But I am getting ahead of myself. There is another chapter in the early development of the archaea
that needs to be told before proceeding further. Prior
to the public announcement of the ‘archaebacteria,’ I
already had some inkling of trouble ahead. It had been
relatively easy to convince those involved directly in
the project that the archaebacteria were a group apart.
They knew the data, and they knew it required explanation; it could not be dismissed. Ralph Wolfe
was soon convinced and got into the habit of giving a
brief ‘peek’ into the future at the end of his seminars
– gentle, but tactful persuasion. My post-doc George
Fox, who was involved in labeling and preparing the
16S rRNA for analysis, Bill Balch, Ralph’s student,
who actually grew the methanogens – it required a special technology Bill and Ralph had developed to do the
job – and Linda Magrum, the technician who worked
in the trenches to generate the Sanger two-dimensional
oligonucleotide patterns; all of them became ready
converts to the new perspective. But outside of this
inner circle, attitudes were quite different. I remember
asking a number of my colleagues what they thought
something that was neither a prokaryote nor a eukaryote would be like. The responses ranged between life
from Mars to something with an RNA genome. No one
could imagine that there could be anything microbial
that was not phylogenetically a ‘prokaryote’!
Then one day (prior to our results being published) Ralph Wolfe showed up with Otto Kandler,
the well-known German microbiologist and botanist,
who wanted to hear our story. George Fox and I were
prepared for the usual frustrating struggle to get the
visitor to realize that there just might be something
under the sun other than E. coli and company in the
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bacterial world. You can imagine our surprise when
shortly after beginning our sales pitch Kandler’s eyes
widened and he said ‘Of course!,’ or something like
that. He had an open mind and a great feel for biology.
That, it turned out was exactly what the archaea
needed to push the concept into the mainstream.
Kandler returned to Germany full of enthusiasm about
‘archaebacteria,’ and proceeded to use his considerable prestige and power in the German microbiology
establishment to help German microbiologists see the
validity and great potential in the archaebacteria. It
was not long before Kandler had organized the first
ever symposium on ‘archaebacteria,’ in Munich. This
was 1981, and Kandler saw to it that the manuscripts resulting from the symposium presentations
were published back to back in two successive issues of the journal Systematic and Applied Microbiology (which at the time still retained its German
name of Zentralblatt für Bakteriologie, Mikrobiologie und Hygiene. 1. Abt. Originale C. Allgemeine,
Angewandte und ökologische Mikrobiologie) – the
journal of which he was the editor. Now the archaeal
concept was off and running. In large measure because
of Kandler’s enthusiasm and influence, Germany became the European (if not the world) leader in archaeal
research.
Unbeknownst to me another German scientist,
Wolfram Zillig, an Abteilung Leiter at the Max Planck
Institute in Martinsried, a person who had spent
most of his career on RNA polymerases, had heard
of the archaebacteria, and had set about to examine their RNA polymerases. By his own admission
Zillig had seen the field get bogged down in detail
and his own career winding down into more of the
same. To his great surprise and pleasure, Wolfram
discovered archaebacterial RNA polymerases definitely not to be of the ‘prokaryotic’ type. In fact these
enzymes were reminiscent of the eukaryotic RNA
polymerases (Huet et al. 1983). So instead of going
out with a whimper, his career suddenly exploded into
a great new adventure, both in the lab and around the
world, where he and his young colleague Karl Stetter
set out to find more ‘bugs’ in places that could be
quite dangerous, like hot springs in Iceland (where
both of them almost came to catastrophic ends on
a couple of occasions) (see Figure 2 for a photograph of Wolfram Zillig with Karl Stetter). Stetter
later continued this new swashbuckling brand of field
microbiology – taking trips into the jungles of Thailand, darkest Africa, the bottom of the ocean, and
other inhospitable places, to find new and exciting
Figure 2. Wolfram Zillig (left) and Karl Stetter (right). This photograph was taken at the Archaea Gordon Research Conference,
2001.
thermophilic archaebacteria. Everyone could feel their
excitement.
While our program in rRNA phylogenetic reconstruction had potentially put bacteriology back on the
right track to become, finally, an organismal discipline, there remained one major stumbling block
to overcome in microbial ecology. Even armed with
Beijerinck’s enrichment culturing methodology, microbiologists had been able to detect only a small
fraction of species in the bacterial world (just how
tiny this fraction was would become apparent only
after the fact). If there ever were to be a real bacterial
ecology, niches would have to be definable in organismal (biological) terms, which meant identifying all the
significant microbes therein.
Molecular phylogenetic characterization was obviously a great step in the right direction, but it did not
solve microbial ecologists’ problem completely – far
from it. To do a 16S rRNA characterization, like any
other characterization, the bacterium in question had
to be under control, that is, in pure laboratory culture
– or did it? While all the rest of microbiology was still
fixated on the traditional need to isolate the bacterium
to know anything about it, one person, Norman Pace,
argued that if phylogenetic identification could be
based on the sequence of one molecule (16S rRNA),
then it was only that molecule that required isolation
and characterization. All the crippling limitations associated with having to cultivate the bacterium in order
to know anything significant about it were suddenly
swept away. Genuine microbial ecology could now
become a reality (Olsen et al. 1986).
Pace’s methodology had enormous potential. To
begin with, one could design (fluorescent) oligonuc-
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leotide probes based upon particular regions in a given
16S rRNA sequence that would permit identifying
under the microscope any microbe that carried that
particular 16S rRNA (DeLong et al. 1989). Moreover,
through proper design one could make a set of such
DNA probes that not only identified an individual microorganism as to species, but as to any taxon in the
overlying hierarchy – be it genus, family, order, and so
on. This methodology is arguably the most powerful
technology in the ecologists’ armamentarium.
Bacteriology (which microbiology used to be
called) is in principle an organismal science, just as
are zoology and botany. An organismal science seeks
to understand (naturally defined) groups of organisms
in biological terms – by which is meant not merely
in a structure/function context, but also in terms of
the group’s diversity, its ecology, and how the organisms therein are ancestrally (evolutionarily) related. In
actuality, however, bacteriology never became a fullfledged organismal science, because it was never able
to develop its evolutionary side – and consequently
was never able to develop a real bacterial ecology,
or make sense of the microbial diversity it had uncovered (Stanier and van Niel 1962). The underlying
reason here is that microbiologists failed to develop a
valid bacterial taxonomy. Such was not possible given
the classical bacterial traits upon which it had at the
time to be based (Woese 1987). Thus, microbiologists
could not develop three of the four pillars of their
organismal discipline.
This was a sorry state of affairs, as Roger Stanier
and Cornelis B. van Niel clearly recognized when they
said ‘. . . the abiding intellectual scandal of bacteriology has been the absence of a clear concept of a
bacterium’ (Stanier and van Niel 1962). And that statement is as valid today as it was 40 years ago – although
no one can deny that there has been great progress in
microbiology over the last half century. Yet, none of
it moved bacteriology in the direction of becoming
a real organismal discipline. Quite the opposite. In
an era defined and dominated by molecular biology
(and biochemistry), it was all too easy for a conceptually floundering microbiology to shape itself in the
mechano-reductionist mode; which then made it all
too easy to forget about such ‘theoretical’ matters as
developing a ‘clear concept of a bacterium.’
Unfortunately microbiologists of the mid 20th century, after failing repeatedly to develop a phylogenetic
system (the only way to attain a concept of a bacterium), sought to settle the problem once and for all
by decree, as it were. It was simply asserted that all
‘prokaryotes’ were of a kind, and that by comparing
the properties of ‘prokaryotes’ to those of eukaryotes,
we could understand what a bacterium was (Stanier
and van Niel 1962). Sounds good on the surface, and it
made the problem go away, but it does not stand up to
analysis. By the time that the archaea were discovered
in 1977, microbiology had long forgotten about their
old concern with a natural taxonomy. Their concept of
the world now hinged on the deeply held, but flimsy,
belief that all prokaryotes were of a kind. The discovery of the archaea knocked the pins out from under
that world view (at long last the monophyly of the
prokaryotes had been put to proper experimental test).
No wonder microbiologists were upset when suddenly
confronted with ‘archaebacteria.’
There is a sad irony in all this, namely, as microbiologists were becoming more dogmatic in their
belief that all bacteria are specifically related and as a
consequence had lost interest in the problem of natural
bacterial relationships, the groundwork for determining these relationships by using molecular measures,
was being laid. In the early 1950s Sanger and coworkers had sequenced the first proteins (Sanger and Tuppy
1951; Sanger and Thompson 1953); and molecular
biologists, at least, were becoming aware of how
valuable protein sequence comparisons should be in
determining phylogenetic relationships. In 1958 one
of the great biologists of the day, Francis Crick, said:
Biologists should realize that before long we shall
have a subject which might be called ‘protein taxonomy’ – the study of amino acid sequences of
proteins of an organism and the comparison of
them between species. It can be argued that these
sequences are the most delicate expression possible of the phenotype of an organism and that
vast amounts of evolutionary information may be
hidden away within them. (Crick 1958, p. 142)
But this trenchant insight fell on deafened ears
within the microbiology community, though not
among certain macrobiologists. The latter saw the new
molecular approach as a marvelous tool for confirming and extending the classical phylogenies of plants
and animals. When microbial taxonomists finally did
get into the act, they used (simple) molecular methods for essentially trivial purposes, to make minor
repairs in the poor bacterial taxonomy passed down to
them by classical microbiologists; which were largely
confined to weeding out misclassified species from
genera and properly grouping genera into families.
The compelling vision of their forebears, their over-
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riding concern with building a concept of bacteria
on a comprehensive natural bacterial taxonomy, was
simply gone.
This mix of scientific apathy, hostility, ignorance,
and a reductionist perspective is what the archaea had
to face in coming of age. Yet, truth has a way of triumphing (in science at least), and the archaeal notion
has now found its rightful place in the pantheon of
biological ideas.
A new century, a new era in microbiology
The discovery of the archaea provided the seed for
microbiology’s (bacteriology’s) developing into a fullfledged organismal discipline, a discipline that has an
active and effective interest in evolution, as well as
ecology and microbial diversity. And today that seed
has been planted in fertile genomic soil. The microbiology of the future will be fashioned in large measure
by genomics and evolutionary considerations. The microbial world is the doorway to approaching one of
the truly great biological problems, how cellular life
originated. It is through the microbial world also that
biology will come to understand the biosphere, the dynamics of the global environment. This is all, however,
for the future. Here and now I need to discuss the impact that genomics has had on our understanding of
the archaea and their implications.
The recent deluge of genomic sequence data has
proven almost as confusing as it has bountiful. At least
that is the impression I get from reading some of the
evolutionary conclusions drawn from this wealth of
data. A veritable cottage industry has arisen in trying
to dismantle the archaea through genomics, and in rerooting, uprooting, or completely destroying the basic
structure of the universal phylogenetic tree based upon
rRNA sequence analyses (see Pennisi 1998, 1999).
Thus, it is appropriate that I summarize the evidence
that genomics has brought forth in support of the archaeal grouping and the structure of the phylogenetic
tree.
First let us consider a problem still posed by the
eukaryote–prokaryote dichotomy. The dichotomy actually comprises two assertions, the one phylogenetic,
and the other organizational. The bipartite phylogenetic division of life has, of course, now been disproven.
But its organizational assertion still lingers and remains a source of confusion. The primary observation upon which the dichotomy rests is that under a
light microscope one can distinguish two, and only
two, types of cellular organization. The eukaryotic
cell presents a very distinct, unique picture, with its
membrane-bounded nucleus and various other intracellular compartments. All prokaryote cells, on the
other hand, appear essentially featureless internally
under the microscope. These observations are certainly justifiable reason to see eukaryotes as having a
common and highly unique cellular organization. But
only by a big stretch of the imagination can one then
infer the same to hold for all bacteria; the evidence
defining their ‘common’ structure being entirely negative (Chatton 1937). Yet this is what was concluded,
and this is what many biologist still believe today.
Now I put it to the reader: if the apparent existence of
two types of cellular organization demands two corresponding primary phylogenetic categories, why is it
not the case, then that the certain existence of three
phylogenetic categories requires there to be three distinct types of cellular organization? Granted, archaea
and eubacteria are equally featureless under the light
microscope. So what? On the molecular level the two
can be distinguished from one another just as easily as
either can be from the eukaryote. What does the molecular level tell us about the organization of the two
cell types? Nothing for certain yet, except that the two
types cannot be the same. Perhaps the most tantalizing
and strongest indicator that there exists a unique type
of archaeal cellular organization is the existence of
an archaeal genomic signature, a set of approximately
300 protein coding genes that are found in at least two
major groups of archaea, but nowhere else (Graham
et al. 2000). (The vast majority of these genes have yet
to be assigned function, although sequence motifs in
many of them do suggest general types of roles they
might play.) Let us now turn to some of the specifics
that distinguish the archaea from the eubacteria.
In their metabolisms the two groups differ subtly,
though not dramatically. The eubacteria are far and
away the most metabolically diverse and versatile organisms on this planet. While the euryarchaea show
some metabolic diversity (a good deal of it imported from the eubacteria), they are most notable for
two things, their unique methanogenesis, and the
cofactors that are more or less unique to the group
– for example, the C-1 carriers, coenzyme M, methanofuran, and methanopterin; coenzyme F420, an
electron carrier analogous to NAD; F430, a nickel
containing porphyrin akin to heme and the like; and
methanophenazine, a membrane-bound carrier with
quinone-like function. Significantly, most of the archaeal cofactors seem to be unique in their biosyn-
370
thesis; at least many of the enzymes involved appear
to be home grown, evolved within the archaeal group
(Wolfe 1992). In addition, there are the ‘classically’ observed biochemical uniquenesses; in archaeal
membrane lipids, cell walls, and so on (mentioned
above).
It is in the information processing systems that
the differences between eubacteria and the archaea are
most impressive. First translation: while much of the
componentry of the archaeal translation mechanism
is universal, homologous between the archaea and
eubacteria (and eukaryotes), the archaeal-eubacterial
distinction is readily apparent in their details (sequences). The distinction between the archaeal and
eubacterial versions of a particular molecule is so obvious that it can usually be seen upon gross inspection
of a sequence alignment (Woese et al. 2000) – where
the archaeal and eubacterial versions characteristically differ by the presence or absence of rather large
sequence blocks. In addition, for those columns in
a sequence alignment where composition is highly
conserved, one often sees that the characteristic eubacterial composition differs from that characteristic of
the archaea and vice versa. This nearly qualitative distinction between the two versions of a sequence, this
difference in ‘genre,’ has been designated ‘canonical
pattern’ (Woese et al. 2000). Differences this extreme
are never encountered among the various eubacterial
taxa or among different archaeal taxa (although in each
case there have been three billion years or so, most of
this planet’s history, in which such differences could
have arisen). When the eukaryotic versions of these
universal proteins are brought into the picture, they
are almost always of the archaeal genre (Woese et al.
2000).
In addition to the universal ribosomal proteins,
however, there exists a relatively small cadre that are
characteristic of and found only in eubacteria, while a
somewhat larger set is common and confined solely to
the archaea and eukaryotes, with still a few others that
are confined to eukaryotic ribosomes.
One sees a similar pattern in the archaeal and
eubacterial transcription mechanisms, but with more
(and more conspicuous) exceptions to universality.
The two largest (the catalytic) subunits of the DNAdependent RNA polymerase, beta and beta in eubacterial nomenclature, are clearly universal, and
demonstrate the above canonical pattern (with, again,
eukaryotic sequences being of the archaeal genre)
(Langer et al. 1995). After this, however, precious
little homology is seen between the eubacterial and
the archaeal componentry in the mechanism. What
homology there is, is confined to the third main transcriptional subunit, the so-called alpha subunit (in
eubacterial nomenclature); but the homology is only
partial. Two copies of alpha occur in the eubacterial holoenzyme, whereas in the archaeal case (or
the eukaryotic) two distinct proteins of very different size exist, each present in single copy, with parts
of each showing homology to (somewhat) different
parts of eubacterial alpha (Langer et al. 1995). Over
and above these differences, the archaeal transcription
polymerase exhibits a number of additional (smaller)
subunits, none of which are found in the eubacterial
case, but all of which occur in the eukaryotic enzyme(s). When it comes to transcription initiation,
homology between the archaea and eubacteria is negligible. The two mechanisms use different componentry
(Bell and Jackson 2001), with the eukaryotes once
again showing an augmented version of the archaeal
mechanism.
The most spectacular difference between the archaea and eubacteria, of course, lies in their genome
replication mechanisms. The closely related archaeal
and eukaryotic systems to a first approximation share
no homology with the componentry of their eubacterial counterpart (Olsen and Woese 1996). And in
keeping with what we have seen above, the mechanism of initiation of chromosome replication in the
eubacteria is fundamentally different from that of
the archaea and eukaryotes. The genome replication
mechanism appears to have evolved twice.
Many biologists deduced specific relationship
between the archaea and eubacteria from their both
having circular chromosome structure (which eukaryotes do not). In light of the similarity between
the archaeal and eukaryotic chromosome replication
and its initiation, this conclusion needs revisiting.
Note also in this context that both the eukaryotic
and archaeal (euryarchaeal) chromosomes exhibit nucleosome organization – the single archaeal histone
being a homolog of the four (related) histones that
structure the eukaryotic nucleosome (Reeve et al.
1997).
Finally I would add that a number of phylogenetic
trees based upon whole genomes, confirm the original
contention based upon rRNA sequence analysis that
the archaea are a grouping unto themselves, neither
eubacterial nor eukaryotic in nature (Fitz-Gibbon and
House 1999; Snel et al. 1999).
371
There have been several suggestions to the effect
that the archaea are not a phylogenetically coherent
(i.e., a valid) organismal group, or to the effect that the
archaea arose from a particular eubacterial ancestor –
all based upon anecdotal evidence and particular genomic sequence analyses (Gupta and Golding 1993;
Cavalier-Smith 2002; see Gupta 2003). In the light
of the above (and other) evidence as to the evolutionary coherence of both the archaeal and bacterial
groups and the strong, specific and detailed distinction between them (especially in key elements of their
cellular designs), I do not see how these contrary
claims can have any validity. The burden of proof
surely rests upon those who would like things to be
otherwise.
The archaea are the harbinger of the future of
microbiology, a future based on the knowledge of
phylogenetic relationships. Among other things this
means that microbial ecology can exist in more than
name only. With the great progress in microbial ecology over the last decade, which continues to escalate,
we can now see first hand what having a phylogenetically based discipline can do. But bacterial ecology
alone realizes only a portion of the potential in a
phylogenetically constituted microbiology – one that
has finally become an organismal discipline. Bacterial evolution is just beginning to come to the fore.
And with it will come a fundamental change in all
of biology, for biology is now on the threshold of
answering the great question: ‘Where did we come
from?’
Acknowledgments
I thank Gary Olsen and Claudia Reich for their valuable comments on this manuscript. This paper was
invited and edited by Govindjee.
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